Lower urinary tract reconstruction is an essential tool in the management of severely dysfunctional bladders in children. The incidence of calculi in augmented bladders has been reported in up to 50% of cases. We analyzed our experience with stone formation in this population to assess risk factors and outcomes. We performed a retrospective cohort study of all patients who underwent bladder augmentation from 1988 to 2002 at our institution. Patient demographics, risk factors and management were abstracted from the medical record. A total of 105 patients (58 males and 47 females) were identified. Ileum, colon and stomach were used in 37, 18 and 50 patients, respectively. Median age was 8.0 years. Median followup was 8.4 years. A total of 12 patients (11%) were found to have bladder calculi. Ten patients with ileum (27%), 1 with colon (6%) and 1 with stomach (2%) formed stones. All patients had recurrent urinary tract infections. Nine patients were successfully treated with an endoscopic procedure. Four patients (33%) formed recurrent stones despite saline bladder irrigations. One patient had multiple recurrences but is now stone-free on a daily regimen of 20% urea instillation. Augmentation cystoplasty carries an overall low risk of bladder calculi. Gastrocystoplasty had a significantly lower rate of stone formation than augmentation with ileum and colon. Urinary tract infection is an independent risk factor for stone formation. Endoscopic management is safe and effective in the majority of patients and it may be facilitated by a percutaneous access. Recurrent stones form in some patients despite aggressive medical management.